Ann Lab Med.  2016 Jul;36(4):320-324. 10.3343/alm.2016.36.4.320.

Prediction of Putative Resistance Islands in a Carbapenem-Resistant Acinetobacter baumannii Global Clone 2 Clinical Isolate

• Lee Y
• D'Souza R
• Yong D
• Lee K

• KMID: 2373551
• DOI: http://doi.org/10.3343/alm.2016.36.4.320

Abstract

BACKGROUND
We investigated the whole genome sequence (WGS) of a carbapenem-resistant Acinetobacter baumannii isolate belonging to the global clone 2 (GC2) and predicted resistance islands using a software tool.
METHODS
A. baumannii strain YU-R612 was isolated from the sputum of a 61-yr-old man with sepsis. The WGS of the YU-R612 strain was obtained by using the PacBio RS II Sequencing System (Pacific Biosciences Inc., USA). Antimicrobial resistance genes and resistance islands were analyzed by using ResFinder and Genomic Island Prediction software (GIPSy), respectively.
RESULTS
The YU-R612 genome consisted of a circular chromosome (ca. 4,075 kb) and two plasmids (ca. 74 kb and 5 kb). Its sequence type (ST) under the Oxford scheme was ST191, consistent with assignment to GC2. ResFinder analysis showed that YU-R612 possessed the following resistance genes: four β-lactamase genes bla(ADC-30), bla(OXA-66), bla(OXA-23), and bla(TEM-1); armA, aadA1, and aacA4 as aminoglycoside resistance-encoding genes; aac(6')Ib-cr for fluoroquinolone resistance; msr(E) for macrolide, lincosamide, and streptogramin B resistance; catB8 for phenicol resistance; and sul1 for sulfonamide resistance. By GIPSy analysis, six putative resistant islands (PRIs) were determined on the YU-R612 chromosome. Among them, PRI1 possessed two copies of Tn2009 carrying bla(OXA-23), and PRI5 carried two copies of a class I integron carrying sul1 and armA genes.
CONCLUSIONS
By prediction of resistance islands in the carbapenem-resistant A. baumannii YU-R612 GC2 strain isolated in Korea, PRIs were detected on the chromosome that possessed Tn2009 and class I integrons. The prediction of resistance islands using software tools was useful for analysis of the WGS.

Keyword

Acinetobacter baumannii; Whole genome sequence; GIPSy; Global clone 2

MeSH Terms

Acinetobacter Infections/*drug therapy/microbiology
Acinetobacter baumannii/drug effects/*genetics/isolation & purification
Anti-Bacterial Agents/pharmacology/*therapeutic use
Bacterial Proteins/genetics
Carbapenems/*therapeutic use
DNA, Bacterial/chemistry/*genetics/metabolism
Drug Resistance, Bacterial
Genomic Islands/genetics
Humans
Microbial Sensitivity Tests
Multilocus Sequence Typing
Plasmids/genetics/metabolism
Polymerase Chain Reaction
Sequence Analysis, DNA
Anti-Bacterial Agents
Bacterial Proteins
Carbapenems
DNA, Bacterial

Figure

• 

  Fig. 1 Circular genome comparison showing putative resistance islands predicted for Acinetobacter baumannii strain YU-R612 by GIPSy. The figure was plotted by using A. baumannii AYE strain as a reference and generated by using the Basic Local Alignment Search Tool (BLAST) Ring Image Generator (BRIG) software.Abbreviations: PRI, putative resistance island; GIPSy, Genomic Island Prediction software.

• 

  Fig. 2 Structures of putative resistance island 1 (A) and putative resistance island 5 (B) identified by using GIPSy and an AbaR4-like resistance island (C) in the YU-R612 strain. The short arrows indicate the primers (P1 to P8).

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